I am doing de novo transcriptom assembly of some alga. I judt did the FASTQC analysis and all my sample are "failed" regarding to the percentage of duplicate reads (= 70-80 % in all my files).
I have a total of 600M reads. Is it ok to just put my data to Trinity or is it better to do something about these duplicates reads ? I would say that these duplicates that are probably caused by PCR will just make the assembly run a bit longer, right ?
Thank you for your help :)